# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:12:59 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: ~{N}-(1,3-benzodioxol-5-yl)-~{N}-methyl-3-[(3-methylphenyl)methyl]-6-oxidanyl-1~{H}-indazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)c1cc2c(Cc3cccc(C)c3)n[nH]c2cc1O)c4ccc5OCOc5c4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 C4K  C4K  ~{N}-(1,3-benzodioxol-5-yl)-~{N}-methyl-3-[(3-methylphenyl)methyl]-6-oxidanyl-1~{H}-indazole-5-carboxamide  ligand  52  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C4K
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 C4K  C1   C  CR6   0  -0.209   0.6336   1.9521   0.2288
 C4K  C2   C  CR6   0   0.356   1.0316   3.3238   0.1404
 C4K  C3   C  CR16  0  -0.407   2.3480   3.6982   0.3285
 C4K  O5   O  OH1   0  -0.637   0.1414   4.2814  -0.1498
 C4K  C8   C  CR56  0  -0.104   2.8676   1.3537   0.8486
 C4K  C9   C  CR56  0   0.448   3.2550   2.6934   0.6697
 C4K  C12  C  CR5   0   0.249   4.0671   0.6723   1.2173
 C4K  C13  C  CH2   0  -0.603   4.2287  -0.7765   1.5410
 C4K  C14  C  CR6   0   0.134   3.6003  -1.6667   0.4963
 C4K  C15  C  CR16  0  -0.305   4.0606  -1.6436  -0.8190
 C4K  C16  C  CR16  0  -0.315   2.3825  -3.2536  -1.4443
 C4K  C19  C  CR16  0  -0.365   2.5328  -2.4947   0.8191
 C4K  C21  C  CR16  0  -0.347  -4.6248  -0.0844  -1.6876
 C4K  C22  C  CR16  0  -0.283  -3.2901   0.3346  -1.6611
 C4K  C24  C  CR16  0  -0.363  -2.9391  -0.6904   0.5135
 C4K  N25  N  NT    0  -0.555  -1.1015   0.4399  -0.5968
 C4K  C27  C  CR56  0   0.305  -5.0752  -0.7952  -0.6027
 C4K  C30  C  CH2   0   0.071  -6.2209  -2.0590   0.8245
 C4K  C4   C  CR16  0  -0.329   1.5453   0.9903   0.6208
 C4K  C6   C  C     0   0.549  -0.7895   1.6152  -0.0082
 C4K  O7   O  O     0  -0.512  -1.6723   2.4076   0.3347
 C4K  N10  N  NR15  0  -0.562   4.5784   2.7238   0.9228
 C4K  N11  N  N     0  -0.257   5.0670   1.5123   1.2464
 C4K  C17  C  CR6   0   0.102   1.9074  -3.2945  -0.1382
 C4K  C18  C  CR16  0  -0.224   3.4549  -2.4350  -1.7809
 C4K  C23  C  CR6   0   0.297  -2.4692   0.0382  -0.5868
 C4K  C26  C  CH3   0  -0.559  -0.2022  -0.3940  -1.3829
 C4K  C28  C  CR56  0   0.303  -4.2511  -1.0896   0.4723
 C4K  O29  O  O     0  -0.485  -4.9507  -1.7803   1.4015
 C4K  O31  O  O     0  -0.484  -6.3104  -1.2965  -0.3729
 C4K  H1   H  HCR6  0   0.276   2.6434   4.7356   0.2387
 C4K  H2   H  HOH1  0   0.474  -0.7545   3.9129  -0.0198
 C4K  H3   H  HCH2  0   0.273   5.2940  -0.9959   1.6422
 C4K  H4   H  HCH2  0   0.271   3.7738  -0.9849   2.5132
 C4K  H5   H  HCR6  0   0.246   4.8899  -1.0003  -1.0906
 C4K  H6   H  HCR6  0   0.246   1.9087  -3.8614  -2.2062
 C4K  H7   H  HCR6  0   0.249   2.1667  -2.5090   1.8410
 C4K  H8   H  HCH3  0   0.251   1.0725  -5.0085   0.8609
 C4K  H9   H  HCH3  0   0.239   0.0059  -3.6173   0.8216
 C4K  H10  H  HCH3  0   0.245   0.2513  -4.5780  -0.6358
 C4K  H12  H  HCR6  0   0.266  -2.8945   0.8971  -2.4970
 C4K  H13  H  HCR6  0   0.277  -2.2923  -0.9211   1.3497
 C4K  H14  H  HCH2  0   0.237  -6.2973  -3.1258   0.5924
 C4K  H15  H  HCH2  0   0.246  -7.0123  -1.7597   1.5123
 C4K  H16  H  HCR6  0   0.276   1.2331  -0.0362   0.7588
 C4K  H17  H  HNR5  0   0.416   5.1970   3.5171   0.8939
 C4K  H18  H  HCR6  0   0.252   3.8140  -2.4132  -2.8020
 C4K  H19  H  HCH3  0   0.255   0.0852  -1.3035  -0.8536
 C4K  H20  H  HCH3  0   0.272  -0.7094  -0.6833  -2.3018
 C4K  H21  H  HCH3  0   0.269   0.6981   0.1477  -1.6559
 C4K  C20  C  CH3   0  -0.723   0.7481  -4.1690   0.2429
 C4K  H11  H  HCR6  0   0.279  -5.2693   0.1509  -2.5234

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 C4K  C26  N25  single    1.457  0.020  1.457
 C4K  O7   C6   double    1.235  0.020  1.235
 C4K  N25  C6   single    1.351  0.020  1.351
 C4K  N25  C23  single    1.425  0.020  1.425
 C4K  C6   C1   single    1.481  0.020  1.481
 C4K  C16  C18  aromatic  1.390  0.020  1.390
 C4K  C16  C17  aromatic  1.390  0.020  1.390
 C4K  C18  C15  aromatic  1.385  0.020  1.385
 C4K  C22  C23  aromatic  1.384  0.020  1.384
 C4K  C22  C21  aromatic  1.399  0.020  1.399
 C4K  C23  C24  aromatic  1.401  0.020  1.401
 C4K  C1   C4   aromatic  1.382  0.020  1.382
 C4K  C1   C2   aromatic  1.431  0.020  1.431
 C4K  C20  C17  single    1.501  0.020  1.501
 C4K  O5   C2   single    1.339  0.020  1.339
 C4K  C17  C19  aromatic  1.395  0.020  1.395
 C4K  C21  C27  aromatic  1.373  0.020  1.373
 C4K  C15  C14  aromatic  1.394  0.020  1.394
 C4K  C4   C8   aromatic  1.390  0.020  1.390
 C4K  C2   C3   aromatic  1.381  0.020  1.381
 C4K  C24  C28  aromatic  1.372  0.020  1.372
 C4K  C19  C14  aromatic  1.389  0.020  1.389
 C4K  C14  C13  single    1.509  0.020  1.509
 C4K  C27  C28  aromatic  1.386  0.020  1.386
 C4K  C27  O31  single    1.353  0.020  1.353
 C4K  C28  O29  single    1.353  0.020  1.353
 C4K  C8   C9   aromatic  1.406  0.020  1.406
 C4K  C8   C12  aromatic  1.428  0.020  1.428
 C4K  C3   C9   aromatic  1.396  0.020  1.396
 C4K  O31  C30  single    1.422  0.020  1.422
 C4K  C9   N10  aromatic  1.348  0.020  1.348
 C4K  C13  C12  single    1.493  0.020  1.493
 C4K  C12  N11  aromatic  1.306  0.020  1.306
 C4K  O29  C30  single    1.423  0.020  1.423
 C4K  N10  N11  aromatic  1.346  0.020  1.346
 C4K  C3   H1   single    0.930  0.020  1.080
 C4K  O5   H2   single    0.850  0.020  0.980
 C4K  C13  H3   single    0.970  0.020  1.090
 C4K  C13  H4   single    0.970  0.020  1.090
 C4K  C15  H5   single    0.930  0.020  1.080
 C4K  C16  H6   single    0.930  0.020  1.080
 C4K  C19  H7   single    0.930  0.020  1.080
 C4K  C20  H8   single    0.970  0.020  1.090
 C4K  C20  H9   single    0.970  0.020  1.090
 C4K  C20  H10  single    0.970  0.020  1.090
 C4K  C21  H11  single    0.930  0.020  1.080
 C4K  C22  H12  single    0.930  0.020  1.080
 C4K  C24  H13  single    0.930  0.020  1.080
 C4K  C30  H14  single    0.970  0.020  1.090
 C4K  C30  H15  single    0.970  0.020  1.090
 C4K  C4   H16  single    0.930  0.020  1.080
 C4K  N10  H17  single    0.860  0.020  1.020
 C4K  C18  H18  single    0.930  0.020  1.080
 C4K  C26  H19  single    0.970  0.020  1.090
 C4K  C26  H20  single    0.970  0.020  1.090
 C4K  C26  H21  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 C4K  C6   C1   C4   121.39  3.000
 C4K  C4   C1   C2   120.07  3.000
 C4K  C6   C1   C2   118.38  3.000
 C4K  O5   C2   C3   117.98  3.000
 C4K  C3   C2   C1   121.09  3.000
 C4K  O5   C2   C1   120.92  3.000
 C4K  H1   C3   C9   122.19  3.000
 C4K  H1   C3   C2   120.57  3.000
 C4K  C9   C3   C2   117.22  3.000
 C4K  H2   O5   C2   108.11  3.000
 C4K  C4   C8   C12  135.77  3.000
 C4K  C12  C8   C9   104.84  3.000
 C4K  C4   C8   C9   119.36  3.000
 C4K  N10  C9   C8   105.55  3.000
 C4K  N10  C9   C3   131.89  3.000
 C4K  C8   C9   C3   122.54  3.000
 C4K  N11  C12  C13  122.43  3.000
 C4K  N11  C12  C8   109.99  3.000
 C4K  C13  C12  C8   127.58  3.000
 C4K  H4   C13  H3   106.56  3.000
 C4K  H4   C13  C14  109.26  3.000
 C4K  H3   C13  C14  110.59  3.000
 C4K  H4   C13  C12  109.43  3.000
 C4K  H3   C13  C12  108.69  3.000
 C4K  C14  C13  C12  112.15  3.000
 C4K  C19  C14  C15  118.88  3.000
 C4K  C19  C14  C13  120.71  3.000
 C4K  C15  C14  C13  120.39  3.000
 C4K  H5   C15  C18  119.97  3.000
 C4K  H5   C15  C14  119.93  3.000
 C4K  C18  C15  C14  120.10  3.000
 C4K  H6   C16  C18  119.81  3.000
 C4K  H6   C16  C17  119.64  3.000
 C4K  C18  C16  C17  120.55  3.000
 C4K  H7   C19  C17  119.15  3.000
 C4K  H7   C19  C14  119.06  3.000
 C4K  C17  C19  C14  121.78  3.000
 C4K  H11  C21  C27  121.87  3.000
 C4K  H11  C21  C22  121.20  3.000
 C4K  C27  C21  C22  116.94  3.000
 C4K  H12  C22  C23  119.59  3.000
 C4K  H12  C22  C21  119.32  3.000
 C4K  C23  C22  C21  121.09  3.000
 C4K  H13  C24  C28  122.20  3.000
 C4K  H13  C24  C23  121.15  3.000
 C4K  C28  C24  C23  116.65  3.000
 C4K  C26  N25  C23  115.77  3.000
 C4K  C23  N25  C6   117.62  3.000
 C4K  C26  N25  C6   126.19  3.000
 C4K  O31  C27  C28  109.41  3.000
 C4K  O31  C27  C21  128.73  3.000
 C4K  C28  C27  C21  121.86  3.000
 C4K  H15  C30  H14  110.53  3.000
 C4K  H15  C30  O31  109.77  3.000
 C4K  H14  C30  O31  109.85  3.000
 C4K  H15  C30  O29  109.78  3.000
 C4K  H14  C30  O29  109.83  3.000
 C4K  O31  C30  O29  107.02  3.000
 C4K  H16  C4   C8   120.11  3.000
 C4K  H16  C4   C1   120.41  3.000
 C4K  C8   C4   C1   119.48  3.000
 C4K  O7   C6   N25  120.94  3.000
 C4K  N25  C6   C1   119.30  3.000
 C4K  O7   C6   C1   119.76  3.000
 C4K  H17  N10  N11  119.56  3.000
 C4K  H17  N10  C9   128.02  3.000
 C4K  N11  N10  C9   112.42  3.000
 C4K  N10  N11  C12  107.20  3.000
 C4K  C20  C17  C19  120.38  3.000
 C4K  C19  C17  C16  118.32  3.000
 C4K  C20  C17  C16  121.29  3.000
 C4K  H18  C18  C16  119.74  3.000
 C4K  H18  C18  C15  119.89  3.000
 C4K  C16  C18  C15  120.37  3.000
 C4K  N25  C23  C24  118.29  3.000
 C4K  C24  C23  C22  121.47  3.000
 C4K  N25  C23  C22  120.22  3.000
 C4K  H21  C26  H20  107.86  3.000
 C4K  H21  C26  H19  108.64  3.000
 C4K  H20  C26  H19  108.10  3.000
 C4K  H21  C26  N25  111.23  3.000
 C4K  H20  C26  N25  108.66  3.000
 C4K  H19  C26  N25  112.22  3.000
 C4K  O29  C28  C27  109.49  3.000
 C4K  O29  C28  C24  128.50  3.000
 C4K  C27  C28  C24  122.00  3.000
 C4K  C28  O29  C30  106.45  3.000
 C4K  C30  O31  C27  106.51  3.000
 C4K  H10  C20  H9   107.91  3.000
 C4K  H10  C20  H8   107.67  3.000
 C4K  H9   C20  H8   106.90  3.000
 C4K  H10  C20  C17  111.48  3.000
 C4K  H9   C20  C17  111.43  3.000
 C4K  H8   C20  C17  111.23  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 C4K  CONST_01  C9   C8   C4   C1     0.00   0.0  0
 C4K  CONST_02  C12  C8   C4   C1   180.00   0.0  0
 C4K  CONST_03  C9   C3   C2   C1     0.00   0.0  0
 C4K  CONST_04  C8   C4   C1   C2     0.00   0.0  0
 C4K  CONST_05  C8   C9   C3   C2     0.00   0.0  0
 C4K  CONST_06  N10  C9   C3   C2   180.00   0.0  0
 C4K  CONST_07  C4   C1   C2   C3     0.00   0.0  0
 C4K  CONST_08  C4   C8   C9   C3     0.00   0.0  0
 C4K  CONST_09  C12  C8   C9   C3   180.00   0.0  0
 C4K  CONST_10  N11  N10  C9   C3   180.00   0.0  0
 C4K  CONST_11  N11  N10  C9   C8     0.00   0.0  0
 C4K  CONST_12  N10  N11  C12  C8     0.00   0.0  0
 C4K  CONST_13  N11  C12  C8   C9     0.00   0.0  0
 C4K  CONST_14  C12  N11  N10  C9     0.00   0.0  0
 C4K  CONST_15  N10  C9   C8   C12    0.00   0.0  0
 C4K  CONST_16  C16  C18  C15  C14    0.00   0.0  0
 C4K  CONST_17  C16  C17  C19  C14    0.00   0.0  0
 C4K  CONST_18  C17  C16  C18  C15    0.00   0.0  0
 C4K  CONST_19  C17  C19  C14  C15    0.00   0.0  0
 C4K  CONST_20  C18  C16  C17  C19    0.00   0.0  0
 C4K  CONST_21  C18  C15  C14  C19    0.00   0.0  0
 C4K  CONST_22  C24  C23  C22  C21    0.00   0.0  0
 C4K  CONST_23  C24  C28  C27  C21    0.00   0.0  0
 C4K  CONST_24  C28  C24  C23  C22    0.00   0.0  0
 C4K  CONST_25  C28  C27  C21  C22    0.00   0.0  0
 C4K  CONST_26  C23  C22  C21  C27    0.00   0.0  0
 C4K  CONST_27  C23  C24  C28  C27    0.00   0.0  0
 C4K  CONST_28  N10  C9   C8   C4   180.00   0.0  0
 C4K  CONST_29  N11  C12  C8   C4   180.00   0.0  0
 C4K  CONST_30  C6   C1   C2   C3   180.00   0.0  0
 C4K  CONST_31  C4   C1   C2   O5   180.00   0.0  0
 C4K  CONST_32  C9   C3   C2   O5   180.00   0.0  0
 C4K  CONST_33  C6   C1   C4   C8   180.00   0.0  0
 C4K  CONST_34  C13  C12  C8   C9   180.00   0.0  0
 C4K  CONST_35  C18  C15  C14  C13  180.00   0.0  0
 C4K  CONST_36  C17  C19  C14  C13  180.00   0.0  0
 C4K  CONST_37  C4   C8   C12  C13    0.00   0.0  0
 C4K  CONST_38  N10  N11  C12  C13  180.00   0.0  0
 C4K  CONST_39  C20  C17  C19  C14  180.00   0.0  0
 C4K  CONST_40  C18  C16  C17  C20  180.00   0.0  0
 C4K  CONST_41  N25  C23  C22  C21  180.00   0.0  0
 C4K  CONST_42  C28  C24  C23  N25  180.00   0.0  0
 C4K  CONST_43  H1   C3   C2   C1   180.00   0.0  0
 C4K  CONST_44  H16  C4   C1   C2   180.00   0.0  0
 C4K  CONST_45  H17  N10  C9   C3     0.00   0.0  0
 C4K  CONST_46  H18  C18  C15  C14  180.00   0.0  0
 C4K  CONST_47  H6   C16  C18  C15  180.00   0.0  0
 C4K  CONST_48  H7   C19  C14  C15  180.00   0.0  0
 C4K  CONST_49  H5   C15  C18  C16  180.00   0.0  0
 C4K  CONST_50  H13  C24  C23  C22  180.00   0.0  0
 C4K  CONST_51  H12  C22  C23  C24  180.00   0.0  0
 C4K  CONST_52  H11  C21  C22  C23  180.00   0.0  0
 C4K  CONST_53  C23  N25  C6   C1   180.00   0.0  0
 C4K  CONST_59  C23  N25  C6   O7     0.00   0.0  0
 C4K  Var_01    O29  C30  O31  C27   10.27  30.0  1
 C4K  Var_02    C28  C27  O31  C30   -6.41  30.0  1
 C4K  Var_03    O31  C30  O29  C28  -10.32  30.0  1
 C4K  Var_04    C14  C13  C12  C8    49.47  30.0  1
 C4K  Var_05    C15  C14  C13  C12   61.95  30.0  3
 C4K  Var_06    O7   C6   C1   C2   -33.76  30.0  2
 C4K  Var_07    H8   C20  C17  C16  109.41  30.0  2
 C4K  Var_08    H19  C26  N25  C23  -79.64  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 C4K  plan-1  C13  0.020
 C4K  plan-1  C14  0.020
 C4K  plan-1  C15  0.020
 C4K  plan-1  C16  0.020
 C4K  plan-1  C19  0.020
 C4K  plan-1  C17  0.020
 C4K  plan-1  C18  0.020
 C4K  plan-1  H5   0.020
 C4K  plan-1  H6   0.020
 C4K  plan-1  H7   0.020
 C4K  plan-1  H18  0.020
 C4K  plan-1  C20  0.020
 C4K  plan-2  C1   0.020
 C4K  plan-2  C2   0.020
 C4K  plan-2  C3   0.020
 C4K  plan-2  O5   0.020
 C4K  plan-2  C8   0.020
 C4K  plan-2  C9   0.020
 C4K  plan-2  C12  0.020
 C4K  plan-2  C13  0.020
 C4K  plan-2  C4   0.020
 C4K  plan-2  C6   0.020
 C4K  plan-2  N10  0.020
 C4K  plan-2  N11  0.020
 C4K  plan-2  H1   0.020
 C4K  plan-2  H16  0.020
 C4K  plan-2  H17  0.020
 C4K  plan-3  C21  0.020
 C4K  plan-3  C22  0.020
 C4K  plan-3  C24  0.020
 C4K  plan-3  N25  0.020
 C4K  plan-3  C27  0.020
 C4K  plan-3  C23  0.020
 C4K  plan-3  C28  0.020
 C4K  plan-3  O29  0.020
 C4K  plan-3  O31  0.020
 C4K  plan-3  H12  0.020
 C4K  plan-3  H13  0.020
 C4K  plan-3  H11  0.020
 C4K  plan-4  C1   0.020
 C4K  plan-4  N25  0.020
 C4K  plan-4  C6   0.020
 C4K  plan-4  O7   0.020
 C4K  plan-4  C23  0.020
 C4K  plan-4  C26  0.020

